ya Sysinfo reports no fpu & mmu mind you it doesn't see my 060 either as it picks it up as an 040...I remember Sysspeed was much more accurate but don't know if it fits on a disk? have to check that out
Not in front of my Amiga right now but pretty sure the latest version of SysInfo (4.0) can properly detect an 060. Anyhow, just suggested it since I know most Amiga users have it, of course there are better tools, lol.
Definitely sounds like an 060 library problem. Or off-hand, maybe SetPatch needs to activate something? Or try using the CPU command? Dunno, I haven't slept over 24 hours so probably am not very much help.

Try THoR's libraries?